Job ID = 10480744 sra ファイルのダウンロード中... Completed: 766262K bytes transferred in 54 seconds (115722K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 30487113 spots for /home/okishinya/chipatlas/results/dm3/SRX3380803/SRR6278166.sra Written 30487113 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:29 30487113 reads; of these: 30487113 (100.00%) were unpaired; of these: 1599249 (5.25%) aligned 0 times 26089671 (85.58%) aligned exactly 1 time 2798193 (9.18%) aligned >1 times 94.75% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 25704862 / 28887864 = 0.8898 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 16 Mar 2018 08:01:29: # Command line: callpeak -t SRX3380803.bam -f BAM -g dm -n SRX3380803.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380803.10 # format = BAM # ChIP-seq file = ['SRX3380803.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Mar 2018 08:01:29: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:01:29: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:01:29: # Command line: callpeak -t SRX3380803.bam -f BAM -g dm -n SRX3380803.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380803.05 # format = BAM # ChIP-seq file = ['SRX3380803.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Mar 2018 08:01:29: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:01:29: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:01:29: # Command line: callpeak -t SRX3380803.bam -f BAM -g dm -n SRX3380803.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380803.20 # format = BAM # ChIP-seq file = ['SRX3380803.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 16 Mar 2018 08:01:29: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:01:29: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:01:36: 1000000 INFO @ Fri, 16 Mar 2018 08:01:36: 1000000 INFO @ Fri, 16 Mar 2018 08:01:36: 1000000 INFO @ Fri, 16 Mar 2018 08:01:42: 2000000 INFO @ Fri, 16 Mar 2018 08:01:44: 2000000 INFO @ Fri, 16 Mar 2018 08:01:44: 2000000 INFO @ Fri, 16 Mar 2018 08:01:49: 3000000 INFO @ Fri, 16 Mar 2018 08:01:50: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:01:50: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:01:50: #1 total tags in treatment: 3183002 INFO @ Fri, 16 Mar 2018 08:01:50: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:01:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:01:50: #1 tags after filtering in treatment: 3183002 INFO @ Fri, 16 Mar 2018 08:01:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:01:50: #1 finished! INFO @ Fri, 16 Mar 2018 08:01:50: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:01:51: #2 number of paired peaks: 5446 INFO @ Fri, 16 Mar 2018 08:01:51: start model_add_line... INFO @ Fri, 16 Mar 2018 08:01:51: start X-correlation... INFO @ Fri, 16 Mar 2018 08:01:51: end of X-cor INFO @ Fri, 16 Mar 2018 08:01:51: #2 finished! INFO @ Fri, 16 Mar 2018 08:01:51: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Mar 2018 08:01:51: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Mar 2018 08:01:51: #2.2 Generate R script for model : SRX3380803.10_model.r INFO @ Fri, 16 Mar 2018 08:01:51: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:01:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:01:52: 3000000 INFO @ Fri, 16 Mar 2018 08:01:52: 3000000 INFO @ Fri, 16 Mar 2018 08:01:53: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:01:53: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:01:53: #1 total tags in treatment: 3183002 INFO @ Fri, 16 Mar 2018 08:01:53: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:01:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:01:53: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:01:53: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:01:53: #1 total tags in treatment: 3183002 INFO @ Fri, 16 Mar 2018 08:01:53: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:01:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:01:53: #1 tags after filtering in treatment: 3183002 INFO @ Fri, 16 Mar 2018 08:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:01:53: #1 finished! INFO @ Fri, 16 Mar 2018 08:01:53: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:01:53: #1 tags after filtering in treatment: 3183002 INFO @ Fri, 16 Mar 2018 08:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:01:53: #1 finished! INFO @ Fri, 16 Mar 2018 08:01:53: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:01:53: #2 number of paired peaks: 5446 INFO @ Fri, 16 Mar 2018 08:01:53: start model_add_line... INFO @ Fri, 16 Mar 2018 08:01:53: #2 number of paired peaks: 5446 INFO @ Fri, 16 Mar 2018 08:01:53: start model_add_line... INFO @ Fri, 16 Mar 2018 08:01:54: start X-correlation... INFO @ Fri, 16 Mar 2018 08:01:54: end of X-cor INFO @ Fri, 16 Mar 2018 08:01:54: #2 finished! INFO @ Fri, 16 Mar 2018 08:01:54: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Mar 2018 08:01:54: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Mar 2018 08:01:54: #2.2 Generate R script for model : SRX3380803.20_model.r INFO @ Fri, 16 Mar 2018 08:01:54: start X-correlation... INFO @ Fri, 16 Mar 2018 08:01:54: end of X-cor INFO @ Fri, 16 Mar 2018 08:01:54: #2 finished! INFO @ Fri, 16 Mar 2018 08:01:54: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Mar 2018 08:01:54: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Mar 2018 08:01:54: #2.2 Generate R script for model : SRX3380803.05_model.r INFO @ Fri, 16 Mar 2018 08:01:54: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:01:54: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:01:59: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:02:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:02:03: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:02:04: #4 Write output xls file... SRX3380803.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:02:04: #4 Write peak in narrowPeak format file... SRX3380803.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:02:04: #4 Write summits bed file... SRX3380803.10_summits.bed INFO @ Fri, 16 Mar 2018 08:02:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4401 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:02:07: #4 Write output xls file... SRX3380803.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:02:07: #4 Write peak in narrowPeak format file... SRX3380803.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:02:07: #4 Write summits bed file... SRX3380803.05_summits.bed INFO @ Fri, 16 Mar 2018 08:02:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7598 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:02:08: #4 Write output xls file... SRX3380803.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:02:08: #4 Write peak in narrowPeak format file... SRX3380803.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:02:08: #4 Write summits bed file... SRX3380803.20_summits.bed INFO @ Fri, 16 Mar 2018 08:02:08: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1940 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。